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Exam 2 Flashcards

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1
Q

RNA synthesis

A

Transcription

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2
Q

Protein synthesis

A

Translation

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3
Q

_____ can be expressed with different efficiencies

A

Genes

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4
Q

Difference between DNA and RNA?

A

Deoxyribose vs Ribose
Thymine vs Uracil
Double Stranded vs Single Stranded

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5
Q

DNA transcription produces a single-stranded RNA that is _____________ to one strand of DNA

A

complimentary

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6
Q

DNA is transcribed by the enzyme ___ __________ in bacteria

A

RNA polymerase

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7
Q

RNA is synthesized in the __ to __ direction

A

5’ to 3’

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8
Q

mRNA

A

Messenger RNA, codes for proteins

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9
Q

rRNA

A

Ribosomal RNA, form the basic structure of the ribosome and catalyze protein synthesis

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10
Q

tRNA

A

transfer RNA, central to protein synthesis as adaptors between mRNA and amino acids

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11
Q

TBP

A

TATA Binding Protein

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12
Q

____________ _______ in DNA causes DNA supercoiling

A

Superhelical tension

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13
Q

DNA with free end —> one helical turn —>

A

DNA helix must rotate one turn

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14
Q

DNA with fixed ends —> one helical turn —>

A

DNA helix forms one supercoil

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15
Q

Negative supercoiling

A

Helix opening facilitated

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16
Q

Positive supercoiling

A

Helix opening hindered

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17
Q

Every molecule of RNA synthesized by RNA polymerase II is capped at the __ end

A

5’

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18
Q

Eukaryotic polymerase II acts like an

A

RNA factory

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19
Q

In eukaryotes, RNA is spliced _____ transcription

A

after

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20
Q

To produce different proteins from the same DNA sequence, some genes have _________ ________ _______

A

alternate splicing schemes

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21
Q

The 3’ end of eukaryotic mRNA is processed so that a ____________ _________ associated with specific binding proteins is formed.

A

poly-adenine structure

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22
Q

mRNA is transported out of the nucleus through the

A

nuclear pore complex

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23
Q

rRNA precursors are processed into _________ in the _________

A

ribosomes, nucleolus

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24
Q

Redundancy in the genetic code?

A

Multiple codes for one amino acid

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25
Q

_____ possible reading frames in protein synthesis.

A

Three

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26
Q

The genetic code is translated by means of ___ ________ that act ___ _____ ______

A

two adapters, one after another

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27
Q

Large complexes of four rRNA’s and more than 40 small proteins

A

Eukaryotic ribosomes

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28
Q

Each ribosome has ___ binding site for mRNA and _____ binding sites for tRNA

A

one, three

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29
Q

___________ occurs in a four step cycle

A

Translation

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30
Q

Initiation of protein synthesis in eukaryotes requires

A

translation initiation factors and a special initiator tRNA

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31
Q

E, P, and A sites

A

Exit, Polymerization, and Addition

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32
Q

The different cell types of a multicellular organism all contain the same

A

DNA

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33
Q

Transcriptional regulators bind in the

A

DNA major groove

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34
Q

Can gene activation occur at a distance from the transcription start site?

A

Yes

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35
Q

These can cause local alterations in chromatin structure to stimulate transcription initiation

A

Eukaryotic transcriptional activators

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36
Q

Transcriptional regulators can work in a ___________ manner to control gene expression

A

cooperative

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37
Q

A single transcriptional regulator can control the expression of ____ genes in a coordinated fashion

A

many

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38
Q

A combination of transcriptional regulators can induce a differentiated cell to

A

de-differentiate into a pluripotent stem cell

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39
Q

Cellular Metabolism Stage 1

A

Digestion: Breakdown of foods to simple subunits

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40
Q

Cellular Metabolism Stage 2

A

Glycolysis: Breakdown of simple subunits to acetyl CoA; limited amounts of ATP and NADH produced

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41
Q

Cellular Metabolism Stage 3

A

Citric Acid Cycle: Complete oxidation of acetyl CoA to H2O and CO2; large amounts of ATP produced in mitochondrion

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42
Q

Stage 1 of cellular metabolism starts in

A

the digestive tract (saliva, stomach, intestine)

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43
Q

Stage 1 of cellular metabolism finishes in

A

the lysosome of the cell

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44
Q

Glycolysis occurs in the

A

cytosol

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45
Q

Glycolysis produces ATP without a need for

A

O2

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46
Q

Glycolysis converts one molecule of glucose into

A

2 molecules of pyruvate

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47
Q

Glycolysis requires hydrolysis of

A

2 molecules of ATP

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48
Q

Glycolysis produces

A

4 molecules of ATP by condensation

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49
Q

The net gain of glycolysis is

A

2 molecules of ATP per molecule of glucose converted

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50
Q

In glycolysis 2 molecules of NADH are formed from

A

NAD+

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51
Q

Sugars are oxidized ________ to CO2 and water

A

stepwise

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52
Q

In direct burning of sugar in a non living system, all free energy is

A

released as heat; none is stored

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53
Q

In stepwise oxidation of sugar in cells, _____ activation energies are overcome by _______ that work at body temperature

A

small, enzymes

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54
Q

In stepwise oxidation of sugar in cells, some free energy is

A

stored in activated carrier molecules

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55
Q

The breakdown of glucose in glycolysis results in the production of

A

2 pyruvate, 2 ATP, and 2 NADH

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56
Q

Coupled reactions form ___ and ____ in steps 6 and 7 of glycolysis

A

ATP, NADH

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57
Q

The citric acid cycle occurs in

A

the mitochondria of cells

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58
Q

Pyruvate is ______________ by the ________ _____________ _______ to produce acetyl CoA

A

decarboxylated, pyruvate dehydrogenase complex

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59
Q

Acetyl CoA is also produced by

A

lipid breakdown

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60
Q

Acetyl CoA is converted via the citric acid cycle to produce 3 ____, 1 ___, 1_____, and 2 _________ of ___

A

NADH, GTP, FADH2, two molecules of CO2

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61
Q

FADH2 and NADH produced by the citric acid cycle provide electrons to

A

the electron transport chain in the inner mitochondrial membrane, where the energy producing reaction oxidative phosphorylation produces large amounts of ATP

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62
Q

The fatty acid oxidation cycle occurs in

A

the mitochondria

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63
Q

The fatty acid oxidation cycle converts

A

triacylglycerol into acetyl CoA

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64
Q

Each trip through the cycle generates

A

1 acetyl CoA, 1 NADH, 1 FADH2, and shortens the hydrocarbon chain by two carbons

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65
Q

__________ of glycolysis are used in many biosynthetic processes

A

Byproducts

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66
Q

Fatty acids are stored as

A

fat globules in fat cells (animals)

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67
Q

Sugars are stored as ______ in plant chloroplasts

A

starch

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68
Q

Both plants and animals also store glucose in a special polysaccharide called ________. This storage form is for _____ ______

A

glycogen, quick energy

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69
Q

_________ _______________ completes the catabolism of food molecules and occurs in ____________

A

Oxidative phosphorylation, mitochondria

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70
Q

Stage 1 of Oxidative Phosphorylation

A

Energy of electron transport is used to pump protons across the membrane

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71
Q

Stage 2 of Oxidative Phosphorylation

A

Energy in the proton gradient is harnessed by ATP synthase to make ATP

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72
Q

This space contains a highly concentrated mixture of hundreds of enzymes, including those required for the oxidation of pyruvate and fatty acids and for the citric acid cycle.

A

Mitochondrial Matrix

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73
Q

Folded into numerous cristae, this space contains proteins that carry out oxidative phosphorylation, including the electron transport chain and the ATP synthase that makes ATP

A

Mitochondrial inner membrane

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74
Q

Because it contains large channel-forming proteins (called porins), this space is permeable to all molecules of 5000 daltons or less

A

Mitochondrial outer membrane

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75
Q

This space contains several enzymes that use the ATP passing out of the matrix to phosphorylate other nucleotides. It also contains proteins that are released during apoptosis.

A

Mitochondrial intermembrane space

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76
Q

Acetyl CoA is produced in the _____________ ______ from ________ and _____ _____

A

mitochondrial matrix, pyruvate, fatty acids

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77
Q

Mitochondria will often cluster at or near sites of

A

high ATP utilization, ex: cardiac muscle cell

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78
Q

These are produced by oxidation of acetyl CoA in the citric acid cycle and stored in NADH and are then passed to electron transport chains located in the inner mitochondrial membrane

A

High energy electrons

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79
Q

Passage of electrons through the electron transport chain proteins within the inner mitochondrial membrane results in

A

the generation of proton gradient across that membrane

80
Q

_________ _______ _________ produced during the citric acid cycle drive the production of ATP in mitochondria

A

Activated carrier molecules

81
Q

________ _________ is coupled to _________ _______________ to generate ATP as a major energy conversion mechanism occurring in mitochondria

A

Electron transport, oxidative phosphorylation

82
Q

High energy electrons are transferred through three protein complexes in the inner mitochondrial membrane. What are they called?

A

NADH dehydrogenase complex
Cytochrome c reductase complex
Cytochrome c oxidase complex

83
Q

___ ________, another protein located in the inner mitochondrial membrane, converts the chemical potential energy of the ______ ________ to chemical potential energy in the _________ ____ of ___

A

ATP synthase, proton gradient, phosphate bond of ATP

84
Q

ATP synthase is a reversible motor, capable of

A

running in two different directions
ATP synthesis vs ATP hydrolysis

85
Q

The electrochemical proton gradient across the inner mitochondrial membrane is used to drive some

A

coupled transport processes:
voltage gradient drives ADP-ATP exchange
pH gradient drives pyruvate import
pH gradient drives phosphate import

86
Q

NADH produced in the cytosol yields fewer ATP molecules than NADH produced in the mitochondrial matrix because

A

the mitochondrial inner membrane is impermeable to NADH

87
Q

Intracellular signaling pathways can be activated by an _____________ ______ ________

A

extracellular signal molecule

88
Q

Extracellular signal molecules can bind to either ____________ _________ or _____________ _________

A

cell-surface receptors, intracellular receptors

89
Q

Effector Protein: metabolic enzyme

A

Target Cell Response: altered metabolism

90
Q

Effector Protein: cytoskeletal protein

A

Target Cell Response: altered cell shape or movement

91
Q

Effector Protein: transcription regulator

A

Target Cell Response: altered gene expression

92
Q

Four forms of intercellular signaling

A

Endocrine
Paracrine
Synaptic
Contact Dependent

93
Q

Adrenaline (epinephrine)

A

Adrenal gland
Derivative of the amino acid tyrosine
Increases blood pressure, heart rate, and metabolism

94
Q

Cortisol

A

Adrenal gland
Steroid (derivative of cholesterol)
Affects metabolism of proteins, carbohydrates, and lipids in most tissues

95
Q

Heart pacemaker cell + acetylcholine =

A

Decreased rate of firing

96
Q

Salivary gland cell + acetylcholine =

A

Secretion

97
Q

Skeletal muscle cell + acetylcholine =

A

Contraction

98
Q

The role of nitric oxide in smooth muscle relaxation in a blood vessel wall

A

Binds to guanylyl cyclase
GTP —> cyclic GMP
Rapid relaxation of smooth muscle cell

99
Q

Signal molecules that bind to nuclear receptors are usually

A

small and hydrophobic
(cortisol, estradiol, testosterone, thyroxine)

100
Q

Three classes of cell-surface receptors

A

Ion Channel Coupled Receptors
G Protein Coupled Receptors
Enzyme Coupled Receptors

101
Q

Estradiol

A

Ovary
Steroid (derivative of cholesterol)
Induces and maintains secondary female sexual characteristics

102
Q

Insulin

A

B cells of pancreas
Protein
Stimulates glucose uptake, protein synthesis, and lipid synthesis in various cell types

103
Q

Testosterone

A

Testis
Steroid (derivative of cholesterol)
Induces and maintains secondary male sexual characteristics

104
Q

Thyroid hormone (thyroxine)

A

thyroid gland
derivative of the amino acid tyrosine
stimulates metabolism in many cell types

105
Q

Epidermal growth factor (EGF)

A

Local mediator
Various cells
Protein
Stimulates epidermal and many other cell types to proliferate

106
Q

Platelet-derived growth factor (PDGF)

A

Local mediator
Various cells, including blood platelets
Protein
Stimulates many cell types to proliferate

107
Q

Nerve growth factor (NGF)

A

Local mediator
Various innervated tissues
Protein
Promotes survival of certain classes of neurons; promotes their survival and growth of their axons

108
Q

Histamine

A

Local mediator
Mast cells
Derivative of the amino acid histidine
Causes blood vessels to dilate and become leaky, helping to cause inflammation

109
Q

Nitric oxide (NO)

A

Local mediator
Nerve cells; endothelial cells lining blood vessels
Dissolved gas
Causes smooth muscles to relax; regulates nerve cell activity

110
Q

Acetylcholine

A

Neurotransmitter
Nerve terminals
Derivative of choline
Excitatory neurotransmitter at many nerve-muscle synapses and in central nervous system

111
Q

Aminobutyric acid (GABA)

A

Neurotransmitter
Nerve terminals
Derivative of the amino acid glutamic acid
Inhibitory neurotransmitter in central nervous system

112
Q

Delta

A

Contact-dependent signal molecule
Prospective neurons; various other developing cell types
Transmembrane protein
Inhibits neighboring cells from becoming specialized in same way as the signaling cell

113
Q

Conformational change activates

A

receptor protein

114
Q

Activated receptor-cortisol complex moves into

A

nucleus

115
Q

Activated receptor-cortisol complex binds to __________ ______ of target gene and activates _____________

A

regulatory region, transcription

116
Q

Two types of intracellular signaling proteins that act as molecular switches

A

Signaling by protein phosphorylation
Signaling by GTP-binding proteins

117
Q

Barbiturates and benzodiazepines (Valium and ambien)

A

Aminobutyric acid (GABA)
Stimulate GABA-activated ion-channel-coupled receptors
Relief of anxiety; sedation

118
Q

Nicotine

A

Acetylcholine
Stimulates acetylcholine-activated ion-channel-coupled receptors
Constriction of blood vessels; elevation of blood pressure

119
Q

Morphine and heroin

A

Endorphins and enkephalins
Stimulate G-protein-coupled opiate receptors
Analgesia (relief of pain); euphoria

120
Q

Curare

A

Acetylcholine
Blocks acetylcholine-activated ion-channel-coupled receptors
Blockage of neuromuscular transmission, resulting in paralysis

121
Q

Strychnine

A

Glycine
Blocks glycine-activated ion-channel-coupled receptors
Blockage of inhibitory synapses in spinal cord and brain, resulting in seizures and muscle spasm

122
Q

Capsaicin

A

Heat
Stimulates temperature-sensitive ion-channel-coupled receptors
Induces painful, burning sensation; prolonged exposure paradoxically leads to analgesia

123
Q

Menthol

A

Cold
Stimulates temperature-sensitive ion-channel-coupled receptors
In moderate amounts, induces a cool sensation; in higher doses, can cause burning pain

124
Q

An activated G-protein disassembles into

A

two signaling components (alpha subunit, beta-gamma subunit)

125
Q

After activation, the G-protein alpha subunit switches itself off by

A

hydrolyzing it’s bound GTP to GDP

126
Q

In heart pacemaker cells a G-protein-linked receptor couples activation to

A

K+ channel opening

127
Q

G protein-linked receptors can cause release of

A

second messenger signaling molecules

128
Q

Cyclic AMP increases rapidly in response to

A

an extracellular signal in nerve cells

129
Q

__________ stimulates glycogen breakdown in skeletal muscle cells

A

Adrenaline

130
Q

____ _____________ is activated by a rise in cyclic AMP concentration

A

Gene transcription

131
Q

Adrenaline —> heart —>

A

Increase in heart rate and force of contraction

132
Q

Adrenaline —> skeletal muscle —>

A

Glycogen breakdown

133
Q

Adrenaline, glucagon —> fat —>

A

Fat breakdown

134
Q

Adrenocorticotropic hormone (ACTH) —> adrenal gland —>

A

Cortisol secretion

135
Q

_____________ _ activates two signaling pathways

A

Phospholipase C

136
Q

Vasopressin (a peptide hormone) —> liver —>

A

Glycogen breakdown

137
Q

Acetylcholine —> pancreas —>

A

Secretion of amylase (a digestive enzyme)

138
Q

Acetylcholine —> smooth muscle —>

A

Contraction

139
Q

Thrombin (a proteolytic enzyme) —> blood platelets —>

A

Aggregation

140
Q

Fertilization of an egg by a sperm triggers an increase in

A

Cytosolic Ca2+

141
Q

_______ _______ changes the shape of the calmodulin protein

A

Calcium binding

142
Q

Receptor tyrosine kinases (RTKs) are activated by a signal molecule in the form of a

A

Dimer

143
Q

Docking of intracellular signaling proteins on an activated RTK activates the protein

A

Ras

144
Q

Ras activates a

A

MAP-kinase signaling pathway

145
Q

The MAP-kinases signaling pathways results in

A

Changes in protein activity
Changes in gene expression

146
Q

RTKs activates the

A

PI 3-kinase Akt signaling pathway

147
Q

Activated Akt

A

down regulates cell death

148
Q

Growth factor binding to ______ ________ _______ can stimulate cells to grow

A

enzyme receptor kinases

149
Q

Both G Protein coupled receptors and RTKs activate

A

multiple intracellular signaling pathways

150
Q

The Notch receptor itself is a

A

transcription regulator

151
Q

In plants, the ethylene signaling pathway turns on genes by

A

removing inhibition

152
Q

_____________ _________ ________ can integrate multiple signals

A

Intracellular signaling proteins

153
Q

Components of the cytoskeleton

A

Actin filaments, microtubules, intermediate filaments

154
Q

____________ _________ provide rigidity and structural stability to cells

A

Intermediate filaments

155
Q

____________ serve as part of a transport system in the cell

A

Microtubules

156
Q

_____ ________ transport cargo throughout the cell through interaction with microtubules

A

Motor proteins

157
Q

Microtubules also help to

A

position organelles in the cell

158
Q

The cytoskeleton is a dense network of _______ ________ that controls the _____ and ___________ ________ in the cell

A

protein polymers; shape; biochemical activity

159
Q

ropelike fibers with a diameter of about 10 nm; they are made of fibrous intermediate filament proteins. One type of intermediate filament forms a meshwork called the nuclear lamina just beneath the inner nuclear membrane. Other types extend across the cytoplasm, giving cells mechanical strength and distributing the mechanical stresses in an epithelial tissue by spanning the cytoplasm from one cell-cell junction to another. These are very flexible and have great tensile strength. They deform under stress but do not rupture.

A

Intermediate filaments

160
Q

hollow cylinders made of the protein tubulin. They are long and straight and typically have one end attached to a single microtubule-organizing center called a centrosome. With an outer diameter of 25 nm, microtubules are more rigid than actin filaments or intermediate filaments, and they rupture when stretched.

A

Microtubules

161
Q

(also known as microfilaments) are helical polymers of the protein actin. They are flexible structures, with a diameter of about 7 nm, that are organized into a variety of linear bundles, two-dimensional networks, and three-dimensional gels. Although actin filaments are dispersed throughout the cell, they are most highly concentrated in the cortex, the layer of cytoplasm just beneath the plasma membrane.

A

Actin filaments

162
Q

A mutant form of _______ (an intermediate filament) makes skin blister easily

A

Keratin

163
Q

____________ _________ support and strengthen the nuclear envelope

A

Intermediate filaments

164
Q

____________ _________ are string and rope-like

A

Intermediate Filaments

165
Q

____________ _________ form a strong durable network in the cytoplasm of the cell

A

Intermediate Filaments

166
Q

____________ grow out from an organizing center

A

Microtubules

167
Q

____________ are hollow tubes made up of tubulin subunits

A

Microtubules

168
Q

_______ polymerizes from nucleation sites on a centrosome

A

Tubulin

169
Q

tubulin dimer with bound GTP (GTP-tubulin) —> GTP-tubulin dimers add to growing end of microtubule —> addition proceeds faster than GTP hydrolysis by the dimers —> GTP cap

A

Growing microtubule

170
Q

protofilaments containing GDP-tubulin peel away from the microtubule wall —> GDP-tubulin is released to the cytosol —> GDP-tubulin

A

Shrinking microtubule

171
Q

____________ guide the transport of molecules and molecular complexes in the nerve axon

A

Microtubules

172
Q

Backward transport

A

To cell body

173
Q

Outward transport

A

To axon terminal

174
Q

________ and _______ are molecular motors that move along microtubules

A

kinesins and dyneins

175
Q

____________ help position organelles

A

Microtubules

176
Q

Organization of the actin-myosin filaments in the cell facilitates

A

contractility

177
Q

_____ _________ allow animal cells to take on many shapes and have many functions

A

Actin filaments

178
Q

_____ _________ are thin, flexible protein threads

A

Actin filaments

179
Q

___ __________ decreases the stability of the actin polymer

A

ATP hydrolysis

180
Q

____________ (in actin filaments) and _______ ___________ (in microtubules) regulate polymer length in different ways

A

Treadmilling; dynamic instability

181
Q

actin filament
actin monomer —> plus end
minus end

A

treadmilling

182
Q

GTP-tublin —> plus end (GTP cap) —> rapid growth —> loss of GTP cap —> catastrophic shrinkage —> GTP cap reestablished

A

Dynamic instability

183
Q

Actin-binding proteins control the action of

A

actin filaments in vertebrate cells

184
Q

Monomers
Monomer sequestering protein
Nucleating protein
Bundling protein (in filopodia)
Myosin motor protein
Side-binding protein
Capping (plus-end-blocking) protein
Cross-linking protein (in cell cortex)
Severing protein

A

Actin filaments

185
Q

Forces generated by actin filaments in the cortex of the cell drives

A

cell forward motion

186
Q

Cortex under tension —> actin polymerization at plus end protrudes lamellipodium —> movement of unpolymerized chain —> contraction —> myosin motor proteins slide actin filaments —> attachment —> further protrusion

A

Cell forward motion

187
Q

A web of polymerizing actin filaments pushes

A

the leading edge of a lamellipodium forward

188
Q

________ is a motor protein that functions with actin filaments

A

Myosin-I

189
Q

Myosin-II molecules can associate with one another to form

A

myosin-II filaments

190
Q

_______ _________ _________ can slide two actin filaments past each other

A

Bipolar myosin-II filaments

191
Q

Muscles contract by

A

a sliding filament mechanism

192
Q

___ __________ drives myosin-II filaments along an actin filament

A

ATP hydrolysis

193
Q

At the start of the cycle, a myosin head lacking a bound ATP or ADP is attached tightly to an actin filament in a rigor configuration (so
named because it is responsible for rigor mortis, the
rigidity of death). In an actively contracting muscle, this state is very short-lived, being rapidly terminated by the binding of a molecule of ATP to the myosin head

A

Attached

194
Q

A molecule of AlP binds to the large cleft on
the “back” of the myosin head (that is, on the side furthest from the actin filament) and immediately causes a slight change in the conformation of the domains that make up the actin binding site. This reduces the affinity of the head for actin and allows it to move along the filament. (The space drawn here between the head and actin emphasizes
this change, although in reality the head probably remains very close to the actin.)

A

Released

195
Q

The cleft closes like a clam shell around the ATP
molecule, triggering a large shape change that causes the head to be displaced along the actin filament by a distance of about 5 nm. Hydrolysis of ATP occurs, but the ADP and inorganic phosphate (Pi) produced remain tightly bound to the myosin head

A

Cocked

196
Q

A weak binding of the myosin head to a new site on the actin filament causes release of the inorganic phosphate produced by ATP hydrolysis, concomitantly with the tight binding of the head to actin. This release triggers the power stroke - the force-generating change in shape during which the head regains its original conformation. In the course of the power stroke, the head loses its bound ADP, thereby returning to the start of a new cycle.

A

Force-generating

197
Q

At the end of the cycle, the myosin head is again bound tightly to the actin filament in a rigor configuration. Note that the head has moved to a new position on the actin filament, which has slid to the left along the myosin filament.

A

Attached

Cell Bio (3 decks)

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